LC-MS/MS (tandem mass spectrometry) Protein Identification is peptide sequence based and is suitable for immunoprecipitated or SDS gel purified protein sample preparations.
MALDI-Tof/Tof Protein Identification is based on a combined peptide mass fingerprint (PMF) and MS/MS of up to ~ 10 peptides. This approach is most suitable for proteins of interest from 2D gels.
MudPIT: Multi-Dimensional Protein Identification Technology is a peptide based Shotgun or bottom-up tandem mass spectrometric analysis approach to identifying hundreds/thousands of proteins isolated from complex samples like cells, tissues, etc.
Top-down/bottom-up approach for protein identification: Highly purified proteins (either intact or enzymatically digested) are identified (without LC separation) and post translational modifications are characterized on an ultra-high mass resolving power (m/Δm50% >400,000) and ultra-high mass accuracy (1 ppm or better for internally calibrated spectra) FT-ICR mass spectrometer platform using specialized protein fragmentation techniques like Electron Capture Dissociation (ECD) and InfraRed Multi-Photon Dissociation (IRMPD).